Apply Transformation Matrix to Existing Mesh
Mesh.transform

import bpy
from mathutils import Matrix

ob = bpy.context.object
me = ob.data

M = Matrix(((1, 0, 0, 0),
     (0, 0.707, 0.707, 0),
     (0, -0.707, 0.707, 0),
     (1, 0, 0, 1)))

me.transform(M)
me.update()